FastQCFastQC Report
Wed 21 Sep 2016
cond1rep1_S1_L001_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep1_S1_L001_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1777370
Sequences flagged as poor quality0
Sequence length75
%GC48

[OK]Per base sequence quality

Per base quality graph

[OK]Per tile sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[WARN]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC52680.29639298514096674Search with Blastn,more detail
First hit on +100: Mus musculus mitochondrial DNA from Lewis lung carcinoma, complete sequence Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG31350.1763842081277393Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG26010.1463398166954545TruSeq Adapter, Index 1 (100% over 63bp)
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC25730.1447644553469452Search with Blastn,more detail
First hit on 55: Mus musculus myelin basic protein (Mbp), transcript variant 6, mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGAGGACCAATGACGTAGATCGG24600.13840674704760403No hit
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGAGGACCAATGACGTCATGTGG22930.12901084186185205Search with Blastn,more detail
First hit on 15: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACAGATCGGAAGAGCACACGTCTGA21250.11955867377079618Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTC20450.11505764134648384Search with Blastn,more detail
First hit on +100: PREDICTED: Cavia porcellus collagen alpha-1(I) chain-like (LOC100717127), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACACACGACTGATCTCTGGCAGAACTGTACCACATCCGCCTTGGGAGCCGTCCAACACTGCTACTCCTCATCAGT20270.11404490905101358Search with Blastn,more detail
First hit on 18: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pmp22:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%

[FAIL]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TCGTT65600.012.98768220
TTTCG65450.012.96320818
TCGCG14550.012.9311497
CGTTT67950.012.90421921
ACGGC76150.011.887609540
CCACG82850.010.92626938
CACGG86500.010.54729839
CGGCC85000.010.44107741
TTCGT82400.010.29662519
ACCGA66800.09.61892151
CGCGG23800.09.0986538
ATACG26750.09.02421470
CGTCC59500.08.77050522
CGTAC28000.08.49456213
TTACC102150.08.47960628
GACCG76150.08.25139950
GTTTA115300.08.15907326
CGAGG82650.08.07493853
TAACG33000.07.852955310
TGACG77400.07.797083463

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)